F2 p.Ser475=
c.1425T>C · rs2502835555 · VCV1772370
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-05%)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -4.3 |
| Overall | ||
| CADD | 0.333 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,854 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- F2
- Protein
- p.Ser475=
- Coding
- c.1425T>C
- MANE Select
- NM_000506
- dbSNP
- rs2502835555
- Type
- single nucleotide variant
- Location
- chr11:46728790 (GRCh38)
- Gene constraint
- LOEUF 0.552 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 480 PDB
- Residue 475
- the peptidase s1 domain; a β-strand; a disulfide bond
Similar variants
- F2 p.Ala490Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Arg217Gln Uncertain significance ★★ ⚠ same condition
- F2 p.Arg224Cys Uncertain significance ★★ ⚠ same condition
- F2 p.Arg35Trp Uncertain significance ★★ ⚠ same condition
- F2 p.Ile438Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Pro471Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Thr488Met Uncertain significance ★★ ⚠ same condition
- F2 p.Val258Leu Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/f2-p-ser475 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown